MolNFT v1 · #135029 · protein
Slow-and fast-binding inhibitors of thermolysin display different modes of binding. crystallographic analysis of extended phosphonamidate transition-state analogues
5TMN: “Slow-and fast-binding inhibitors of thermolysin display different modes of binding. crystallographic analysis…”. X-ray diffraction, 3 ligands (0PJ, CA, ZN), 1 pocket (best druggability 0.50). MolNFT v1 #135029 on GenesisL1: 3D…
- PDB
- 5TMN
- Type
- protein
- Length
- 316 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermolysin
- EC
- 3.4.24.27
- UniProt
- P00800
- Ligands
- 0PJ, CA, ZN
- Pockets
- 1 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Thermolysin (EC 3.4.24.27) | protein | 316 | 41% helix, 17% strand | P00800 |
Ligands and binding sites
- 0PJ · N-[(S)-({[(benzyloxy)carbonyl]amino}methyl)(hydroxy)phosphoryl]-L-leucyl-L-leucine · ligand · chains E
- CA · Calcium ion · metal · 4 copies · chains E
- ZN · Zinc ion · metal · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.50 | 0.79 | 24 | 0PJ |
Compared structures
- 5TMN · Slow-and fast-binding inhibitors of thermolysin display different modes of binding.… · the same entry in another collection · chain E against E, TM-score 1.00
- P00800 · AlphaFold monomer V2.0 prediction for thermolysin (P00800) · a predicted model of the same protein · chain E against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P00800
- Elsewhere: RCSB PDB 5TMN · PDBe 5TMN · UniProt P00800
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